Genetics Flashcards
the human genome - how many nts, how many genes (what percent of genome is genes)
unique sequence of 3 billion nts (or base pairs), with 20,000-25,0000 genes comprising 1-2% of total genome and many other regions involved in reg/control; mammal genomes not as large as some plants/protists/amphibians etc
human genomes 99.9% identical; at any given genomic locus, all individuals are related on a tree, where on one branch perhaps a G-T mutation occurred, so all other branches G and all from that branch T; diffs between individual correspond to mutations which have occurred since most recent common ancestor eg humans/chimps 1.37% diff, from gorillas 1.75% diff, from orangutans 3.4%
genome evolution - 3 forms of selection, what is genetic drift, how does pop size influence drift, 2 models used to model drift, is selection better or worse in smaller pops and implication for deleterious alleles
natural selection: +ve favours new beneficial allele, negative/purifying favours existing allele, balancing (rare) favours presence of 2 or more alleles
germline mutation introduces new allele at low freq; genetic drift is random variation in allele freq from one gen to next; genetic drift is stronger in smaller pops leading to more loss of genetic diversity
in wright-fisher model of genetic drift, in diploid pop of N individuals, 2N copies of gene with allele freqs q and p, assume generations don’t overlap and each copy of each gene in new gen drawn randomly from all copies of gene in old gen: probability of getting k copies of allele with freq p in last gen is 2N!/k!(2N-k)! x P^k x q^(2N-k); moran model assumes overlapping gens, gives similar results to wright-fisher but genetic drift runs twice as fast (also moran model more complex to computer simulate as needs more time steps); selection is less effective in smaller pops so even deleterious alleles can inc in freq
effects of genetic drift - definition, one dec and one inc due to what phenomena and effect of population size on these phenomena, 3 world examples of this
genetic drift: random changes in allele freq from one gen to next; genetic diversity decreases and homozygosity increases over time due to allele fixation (freq reaches 100%) or loss (freq reaches 0%) with these effects greater (diversity lost more quickly) in smaller populations, and moderately deleterious mutations undergoing negative selection can fix in a small population; in small/isolated pops there is increased prevalence of deleterious pathogenic alleles and less effective negative selection eg amish/hutterite/mennonite communities in north america have inc prevalence of microcephaly, Tay-sachs disease in ashkenazi jews; finnish disease heritage: 33 monogenic diseases more freq in finland than any other population
chi squared and genetics - purpose of using the test; starting assumption, if thi is true what should allele count be; how chi squared calculated and what it will show you once calculated; 2 steps for chi squared in GWAS, how can population structure introduce error
to determine if association between allele and disease: assume no link, if no link, allele count in cases/controls should reflect overall pop (so allele freq x number of controls); then record how the data actually is
chi squared statistic is normalised measure of diff between observed and expected values; (observed value - expected value)^2/expected value; calculate p value using your degree of freedom can see whether difference is due to random variation or if link exists; assumes no bias in data collection etc
in GWAS: calculate chi squared values for many loci, rank them in size of x^2 value and top ones can be considered further; convert chi squared values into p values and set genome wide significance threshold eg 10^-8 (also express as -log10 p >8) and consider all loci with p values less than this; large sample size (thousands) needed to get sufficient statistical power for most phenotypes; population structure can lead to false signals of association: if cases/controls have diff genetic ancestry, will find genetic variants associated with that
mendellian genetics - 3 principles, how to tell if one plant is hom/het; 8 reasons for frequency of trait to not be what is predicted from those 3 principles
principles of segregation (2 alleles, one from each parent, random transmission), independent assortment (except linkage), dominance: back cross of F1 with homozygous recessive to see if dominant is homo/hetero
alterations to frequency if: genotype early lethal, imprinting, epistasis (genes interact to produce phenotype eg ee for blonde labs, usually BB/bb that decides if Ee or EE), dynamic mutation, variable penetrance/expressivity (not all show phenotype, show phenotype to varying degree), linked inheritance, co-dominance (homo/hetero show diff phenotype)
genetic linkage - what it is, how to test, what is a centimorgan, what did it allow for, nowadays what do we do
loci close together will co-segregate so have lower chance of recombination, test if linked using chi squared with null hypothesis that they aren’t linked (ie same recombination frequency as with gene on another chromosome), exception to independent assortment; recombination% (ie % chance they will become separated) converts to distance eg 1% = 1 centimorgan (doesn’t convert to actual distance as eg centromeres less chance of recombination happening)
this allows distance and mapping of genome using markers at known loci to establish candidiates for monogenic disease causing variants then checking to see if mutated in patient; nowadays we can sequence genome and use actual physical distances, look for mutations in patient’s genome etc
genetic tests - 2 common ones; karyotype what it is, 5 detects and 2 misses; fast-FISH what it is, detects 2 and misses 3; QF-PCR what it is, detects 2 and misses 3; microarray what it is, how resolution varies, detects 4 and misses 3;
most children with possible genetic condition will have a genetic test, and most commonly this will be chromosomal microarray or WGS (with important exceptions)
karyotype:
A cytogenetic test to visualise the number and structure of chromosomes
Detects:
Large deletions and duplications (>5Mb)
Chromosomal translocations/rearrangements
Aneuploidies (abnormal number of chromosomes)
Can detect chromosomal mosaicism ~10%
Misses:
Small-moderate sized deletions and duplications (~<5Mb)
Sequence variants, etc.
Fast-FISH
Fluorescence in situ hybridisation (FISH) is a cytogenetic test, which uses chromosome specific probes to identify the common aneuploidies
Detects:
‘Fast-FISH’ is typically the quickest way to detect the common aneuploidies (e.g. Down Syndrome, Edwards Syndrome, Patau’s Syndrome) in the post-natal setting
Some labs will report sex chromosome aneuploidies (e.g. Turner Syndrome, Kleinfelter Syndrome)
Misses:
Copy number variants (microdeletions and duplications) unless using targeted probes
Chromosomal translocations, sequence variants, etc.
QF-PCR
Quantitative Fluorescence PCR is a molecular genetic test which uses chromosome specific markers to identify the common aneuploidies. It is typically used in the pre-natal setting, but some labs may offer post-natally.
Detects:
QF-PCR is typically used in the pre-natal setting to detect the common aneuploidies (e.g. Down Syndrome, Edwards Syndrome, Patau’s Syndrome) in the post-natal setting
Some labs will report sex chromosome aneuploidies (e.g. Turner Syndrome, Kleinfelter Syndrome)
Misses:
Copy number variants (microdeletions and duplications) unless using targeted probes
Chromosomal translocations, sequence variants, etc.
Micro-array
Cytogenetic test, which uses probes across the genetic code to detect imbalances (copy number variants).
The resolution of an array (the size of deletions and duplications it can detect) varies across different regions of the genome, depending on probe density.
SNP array and array CGH are both types of microarray, but are performed using different laboratory techniques.
Detects:
Microdeletions (e.g. 22q11.2 microdeletion, William’s syndrome) and microduplications
Aneuploidies
Can detect chromosomal mosaicism ~>10%
A SNP-based array can detect unipaternal isodisomy, triploidy and loss of heterozygosity
Misses:
Balanced translocations/rearrangements
Small deletions and duplications (~<50Kb)
Sequence variants, etc.
genetic tests part 2 - exome sequencing what it is, 2 ways to analyse, how second way is approached, detects 3 things, misses 9; whole genome sequencing what it is, what panels are, detects 2, misses 3; 6 times specific assays needed instead of general tests
Exome sequencing
A molecular genetic test, which sequences the coding portion of the genetic code (~1% of the entire genome).
An exome can be analysed as a trio (child and parents analysed together) or as a singleton/duo.
The results of a trio exome are usually filtered using an “agnostic approach” (concentrating on variants which are de novo, recessive, or X-linked). A duo or singleton exome is usually filtered using one or more virtual panels.
Detects:
Sequence variants (“spelling mistakes”) in the coding genes
Some exome testing techniques can detect intragenic (small) deletions and duplications
Some exome testing techniques can detect copy number variants
Misses:
A trio exome, which uses an “agnostic” filtering approach, may miss autosomal dominant inherited disorders
An exome which is filtered using virtual panels, may miss variants in genes not included on the panels
Non-coding variants, microdeletions and duplications, aneuploidies, triplet repeat disorders, disorders of methylation/imprinting, mitochondrial mutations, etc.
An exome may miss low level mosaicism, depending on read depth
Whole genome sequencing
A molecular genetic test which sequences the entirety of the genetic code (~3 billion base pairs).
Typically the results of the genome are filtered using one or more virtual panels ie a panel for intellectual disability, another for hyperinsulinism etc - you will generally order a panel rather than the whole test.
As above, the results of a trio genome are usually filtered using an “agnostic approach” (concentrating on variants which are de novo, recessive or X-linked).
Detects:
Sequence variants in both coding and non-coding areas of the genome
Some genome testing techniques can detect intragenic (small) deletions and duplications, and copy number variants
Misses:
A genome, which is filtered using virtual panels, may miss variants in genes not included on the panels
Triplet repeat disorders, disorders of methylation, mitochondrial mutations, etc
A genome may also miss low level mosaicism, depending on read depth
Some conditions need specific assays as none of the above will pick them up, eg:
Methylation disorders (e.g. Prader Willi, Angelman, Beckwith Weidemann and Russell Silver Syndrome)
Spinal Muscular Atrophy
Triplet repeat and other short tandem repeat disorders (e.g. Myotonic dystrophy, Fragile X, Friedrich ataxia, most spinocerebellar ataxias)
Disorders caused by variants in the mitochondrial genome
Uniparental disomy
Deep sequencing on DNA extracted from an affected tissue (e.g. somatic mosaicism in PIK3CA-related disorders)
chromosomal microarray
A microarray is a special genetic test that looks in detail at a person’s chromosomes to see if there are any extra or missing sections which might account for problems they have been experiencing
It can identify:
large deletions and microdeletions and large duplications and microduplications
most abnormalities of chromosome number (eg Down syndrome)
unbalanced rearrangements of chromosome (eg complex insertions or deletions).
However, it does not identify:
single gene mutations
fragile X syndrome (FXS)
balanced rearrangements (eg: translocations and inversions).
There are two different ways of performing microarray testing: array comparative genomic hybridisation (aCGH) and single nucleotide polymorphism array (SNP array).
aCGH
Patient and reference DNA are labelled with different coloured fluorescent dyes (usually red for reference and green for patient DNA).
An array slide is spotted with oligonucleotide DNA probes – small molecules of DNA that are designed to hybridise with a particular section of the genome. Probe distribution around the genome is not even. The probes provide ‘backbone’ coverage around the genome, and additional probes may be present in gene rich regions, syndrome regions or specific genes of interest.
Patient and reference DNA are washed over the array slide and bind competitively to the probes.
The array slide is washed and scanned, and the fluorescence emitted at each probe location is measured.
Computer software then analyses the data:
Yellow: equal patient and reference DNA present.
Red: more reference DNA than patient DNA, therefore a deletion is present.
Green: more patient DNA than reference DNA, therefore a duplication is present.
A SNP array slide is spotted with allele-specific DNA probes targeting regions in which there is SNP variation between individuals.
Patient DNA is hybridised to the array slide and binds to the probes.
The array slide is scanned, and the fluorescence emitted at each probe location is measured.
The fluorescence emitted is dependent on which alleles are present in the patient at the SNP site targeted by the probe.
Computer software then analyses the data, identifying regions in which copy number variation is present by looking at which nucleotides are present at each SNP location.
CMA tests should be considered by any clinician evaluating a child with otherwise unexplained developmental delay, intellectual disability, ASD, or congenital anomalies
common conditions tested for using chromosome microarray include: digeorge syndrome, prader willi and angelmans, williams syndrome, ASD (16p11.2 deletion), sotos, cri du chat, charcot marie tooth and more
3 important rules to cover when consenting for genetic test, 2 challenges for testing (inc how many de novo mutations we have), what is a trio/why do it, general what 2 bottles to send
Non-diagnosis: There is no single genetic test that can diagnose all genetic conditions. Even very extensive genetic tests (eg exome or genome sequencing) will miss underlying genetic diagnoses. A “normal” genetic test result cannot entirely rule out an underlying genetic diagnosis.
“Grey results” / Variants of uncertain significance: We all carry thousands of genetic variants (“spelling mistakes”) across our genetic code. Sometimes when the lab detect a variant, it can be difficult for them to work out if the variant is causing a problem (“pathogenic”) or if it is harmless (“benign”). These “grey results” can sometimes cause additional worry or anxiety.
Incidental findings, including unexpected family relationships: It is possible that genetic testing can detect variants which do not explain the original reason for the test, but are still relevant for health (an “incidental finding”). The laboratory do not usually go “looking for” incidental findings, but if they encounter an incidental finding, they may report this back. In general, the lab will only report incidental findings where something can be done (e.g. cancer screening), or where there is value in having forewarning (e.g. reproductive implications). When undertaking genetic testing of parents and children together (eg a trio exome or genome), it is also possible that the lab can detect that the family relationships are not as expected, for example, where the father is not the biological father, or that the parents are close relatives.
another challenge is that we all carry variants inc 60 de novo (ie parents didn’t have) 1-2 of which will be in coding region, but if this doesn’t contribute to disease phenotype is an erroneous result
also one disorder can be caused by many genes eg noonan syndrome (11 genes) and one gene can mutate and cause many different disorders
test results are much better if you send a trio (ie both parent’s samples + kids sample, allows interpretation of de novo change etc; send an EDTA bottle and a green top for each person)
exome sequencing - picks up mutations in which area, 4 steps
picks up mutations in DNA coding for proteins (not regulatory stuff); genomic DNA cleaved into ~500bp fragments, PCR and library then hybridise with exon probes on library DNA, elute what they bind to and PCR to make exome library, sequence and analyse for mutations; recent national project for families with developmental disorders
meiosis - what is the process, what do you end up with; 7 steps in meiosis 1, 5 steps in meiosis 2; what is aneuploidy and why does it occur; 2 ways to classify translocations; what is anaphase lag
Meiosis describes the process of cell division by which gametes are made. In this process, we begin with a cell with double the normal amount of DNA, and end up with 4 non-identical haploid daughter gametes after two divisions.
In meiosis I, homologous chromosomes are separated into two cells such that there is one chromosome (consisting of two chromatids) per chromosome pair in each daughter cell, i.e. two chromosomes total.
Prior to prophase, chromosomes replicate to form sister chromatids. There are initially four chromatids (c) and two chromosomes (n) for each of the 23 chromosome pairs (4c, 2n). The nuclear envelope disintegrates and the chromosomes begin to condense. Spindle fibres appear which are important for the successful division of the chromosomes.
To further increase genetic diversity, homologous chromosomes exchange small parts of themselves, such that one chromosome contains both maternal and paternal DNA. This process is known as crossing over, and the points at which this occurs on a chromosome are referred to as chiasmata.
Prometaphase I
Spindle fibres attach to the chromosomes at points along the chromosomes called centromeres. While this is happening, the chromosomes continue to condense.
Maternal and paternal versions of the same chromosome (homologous chromosomes) align along the equator of the cell. A process called independent assortment occurs – this is when maternal and paternal chromosomes line up and randomly align themselves on either side of the equator. This in turn determines which gamete chromosomes are allocated to, which leads to genetic diversity among offspring.
Anaphase I
Here, each of the homologous chromosomes is pulled towards opposite poles of the cell as the spindle fibres retract. This equally divides the DNA between the two cells which will be formed.
Telophase I and Cytokinesis I
During telophase I, the nuclear envelope reforms and spindle fibres disappear. In cytokinesis I, the cytoplasm and cell divide resulting in two cells that are technically haploid – there is one chromosome and two chromatids for each chromosome (2c, n).
Meiosis II
Prophase II and Prometaphase II
These stages are identical to their counterparts in meiosis I.
Metaphase II
In metaphase II, chromosomes line up in single file along the equator of the cell. This is in contrast to metaphase I, where chromosomes line up in homologous pairs.
Anaphase II
Next, sister chromatids are pulled to opposite poles of the equator.
Telophase II
This stage is the same as telophase I.
Cytokinesis II
Again, the cytoplasm and cell divide producing 2 non-identical haploid daughter cells. As this is happening in both cells produced by meiosis I, the net product is 4 non-identical haploid daughter cells, each containing one chromosome consisting of one chromatid (1c, 1n). These are fully formed gametes.
Abnormalities in chromosome number include aneuploidy, where there is loss or gain of a whole chromosome. This is often due to nondisjunction where there is failed separation of chromosomes during anaphase, so either whole chromosomes (error occurring in meiosis I) or chromatids (error occurring in meiosis II) move to the same pole of the cell. This leaves one gamete short of some genetic information, and the other with additional genetic information.
Abnormalities in chromosome structure are often due to translocations, where there is an exchange of material between two chromosomes, resulting in an abnormal rearrangement. If there is no gain or loss of genetic material, this is a balanced translocation, however, if the exchange of chromosomal material results in extra or missing genes in a daughter cell, it is known as unbalanced and can have clinical effects.
There are two types of chromosomal translocation. Reciprocal translocations take place when the chromosomes break within the arms of the chromosome and Robertsonian translocations take place when whole chromosomes join end to end.
Anaphase lag can occur when chromosomes are left behind due to defects in the spindle fibres or attachment to chromosomes. This differs from non-disjunction as neither cell receives the chromosome/chromatid, leaving both daughter cells short of genetic information.
chromosome aberrations - 2 main types, high aneuploidy incidence in what kind of cr, 2 ways embryo can survive this, commonest compatible with life inc 3 different sources, what is non-disjunction and what does it give; commonest reason for ts21, spont abortion and cr aberrations
numerical or structural, high aneuploidy incidence in sex chromosomes, embryo can only survive if on small chromosomes (like 21) or mosaicism
down syndrome most common compatible with life, 90% maternally inherited, 4% paternally and rest post fertilisation giving mosaicism, possible to have extra part of c21 due to translocation
non-disjunction (failure of homologues to segregate) can give aneuploidy (primary in meiosis 1, secondary in meiosis 2)
ts21 usually primary non-disjunction with increased risk with mother’s age
missing or extra chromosomes is most common cause of spontaneous abortion (>50%), esp in first trimester, can be recurrent
polyploidy - what percent of embryos triploid, commonest cause, another cause; tetraploidy cause, what cells are naturaly polyploid
3% pregnancies have triploid embryo, incompatible with life: dispermy is cause 66% of time, can also be whole genome non-disjunction in sperm or ovum; tetraploidy rarer, always lethal, due to failure to complete first zygotic division (DNA replicated but no cell division - endomitosis)
some cells (trophoblast in placenta) naturally polyploid
translocation mutations - how do they arise, 2 subtypes (amount of material), 2 subtypes (structure), 2 common clinical examples
structural aberration with recombination between non-homologous chromosomes: can be balanced, with no loss or gain of genes and so clinically normal (though increased risk of unbalanced offspring), or unbalanced with loss or gain of genes
can be reciprocal (normal unwanted recombination) or robertsonian with break near centromere of 2 acrocentrics fusing to make a large metacentric and small chromosome which is lost as it has no centromere
95% patients with chronic myelogenous leukaemia have translocation between chromosome 9 and 22 t(9;22)(q34;q11) such that breakpoint cluster region from 22 fused with ABL proto-oncogene of 9 so novel protein (a tyrosine kinase) is generated; balanced translocation of chromosome 21 can give Down syndrome not associated with maternal age
copy number variations - 2 main types, clinical example of this; inversion 2 main types and risk
CNVs include duplications and deletions due to unequal recombination with chromosome segment duplicated or missing; digeorge syndrome (22q11.2) is deletion of part of c22 affecting 1:4000 births
2 breaks can cause 180 degree inversion of segment - paracentric if on one arm and pericentric if involving centromere - usually without clinical abnormality but increased risk of generating unbalanced gametes
X linked inheritance - what cr males and females get from parents and how this links to XL inheritance x3; sex cr non-disjunction syndromes x3; x-linked recessive conditions x3; how to tell if woman is obligate carrier x2; XL dominant pedigree apperance, 2 clinical egs (inc why girls survive the second)
each son must get Y from dad and one of mum’s X’s, each daughter must get dad’s X
males always manifest recessive X-linked, females might not, and no male to male transmission; if dominant X-linked might be fatal to men, all daughters of affected male will have
sex chromosome non-disjunction can give aneuploidies: 1:5000 turner’s syndrome is XO female with webbed neck, short stature, infertile; klinefelters is 1:1000 XXY male, tall and thin with cancer risk, mild learning impairment and infertile; XYY male 1:1000 clinically normal, increased growth, normal testosterone levels and fertility
515 x-linked recessive traits, variable frequency in ethnic groups, red-green colour blindness, always from father to daughter who is usually carrier if mum unaffected so might skip generation; duchenne’s muscular dystrophy with mutation in dystrophin gene start ~age 6 1:3600, progressive muscle weakness and death in twenties with no known cure; haemophilia: a is factor VIII 1:5000, b is factor IX 1:25,000 obligate carrier if daughter of affected father or mother if: has more than one son with condition or one son and one other blood relative
for dom: pedigree resembles autosomal dominant but no male to male transmission; vit D resistant ricketts, Rett syndrome is early lethal so no affected males, 1 in 8000-10,000 girls (survive due to x inactivation, which also means hetero may not be affected) gives seizures, hard to walk, can’t talk
the y chromosome (in general how many gees, what region shared with X, what region determines male sex and what if point mutation or tranlocation of this region; X inactivation why, how determined, 2x consequences, what suggests epigenetic mechanism, what triggers inactivation and what area escapes this x2; what particular epigenetic modification common on activated and inactivated X cr
y chromosome: highly heterochromatic and repetitive with multiple inverted palindromic repeats and gene poor (1% of diploid genome: 60 genes coding for proteins) 2 small regions (psuedoautosomal regions) shared with x that can recombine; SRY gene mapped to smallest bit of Y known to cause maleness, point mutation in it causes XY females and translocation causes XX males; turned female mice into males when injected; SRY initiates testis development
x inactivation: occurs early in placental mammals so not twice amount of gene products; all but one X inactivated, which one is random (could be maternal or paternal) and the condensed one is genetically inactive: consequences of inactivation include patches of hair colour and diluting mutation effects, and a heritable memory of which was inactivated suggests epigenetic mechanism; Xist is non coding RNA that is expressed from the chromosome to be inactivated and initiates inactivation by triggering a hierarchy of epigenetic modifications to condense and heterochromatise the chromosome to repress transcription; pseudoautosomal regions (PAR1/2) at tips of X and Y escape inactivation, can be haploinsufficient; non-PAR genes can also escape inactivation (20% in humans, some of functional Y homologues); histone acetylation strongly present on active X, inactive X undergoes methylation late in inactivation
epigenetics - study of what, how can we tell its heritable, 4 ways histones modified and effect on chromatin (which type is actibe and which inactive), how often does epigentic reprogramming occur and at which stages of dev, what are parental imprints resistant to
study of modification to DNA/chromatin and influence on genome function, both local and long range; maintained during division and thus heritable
histone proteins chemically modified inc activating methylation, acetylation, and deactivating methylation (commonest), deacetylation to open or condense chromatin respectively; inactive thus heterochromatic and active euchromatic; correct modifications essential for centromere function; epigenetic tags can also be direct methylation etc of DNA
epigenetic reprogramming is genome wide, twice in development with epigenetic marks erased by passive and active mechanisms which are re-established during implantation for gene regulation, and new ones added: 1st in developing germ cells, in prospermatogonia during fetal development/ growing oocyte phase, 2nd immediately after fertilisation, parental imprints resistant to this one
genomic imprinting - how many genes have parental imprinting and what form does this take, 2 ways this can lead to disorders and how trait inheritance map looks + eg of gene expressed only from paternal cr, cause of BW syndrome, PW, angelman, what are DMRs and ICRs and how do epimutations interact with ICR to effect imprinting
maternal and paternal chromosomes behave differently as ~1% of genes (~100-200) imprinted, that is to say germline epigenetic modifications silence one copy (say maternal) and other copy thus acts
IGF2 expressed only from paternal chromosome, abnormal imprinting consequently leading to genetic disorders and cancer; DNA methylation is retained as a heritable memory; disorders arise from uniparental disomy (silver-russell syndrome), which can also unmask recessive conditions like CF, and from mutation or epimutation of imprinting controls; trait maps similar to autosomal but sex of parent matters
Beckwith-Wiedemann syndrome is fetal overgrowth, multi-organ hyperplasia and increased incidence of childhood tumors with altered dosage of IGF2 growth factor due to extra paternal chromosome; Prader-Willi syndrome is neurological disorder with weight gain caused by paternally inherited deletion or fault in paternally expressed imprinted gene on cr 15 (paternal copy needed to work as maternal copy is methylated and so silenced), or double maternal inheritance aka uniparental maternal disomy (as both copies will thus be methylated and inactive); Angelman syndrome is neurological/developmental disorder due to loss of maternally expressed genes or (rarely) uniparental paternal disomy in same region of cr15 (opposite problem as P-W but same area)
differently methylated regions DMRs have different methylation pattern compared to similar chromosomes (eg imprinting), not all of them are imprinting control regions ICRs as some established later, but all ICRs are DMRs; many imprinted genes have single ICR to control their expression and if epimutation causes ICR to lose methylation then normal imprinting is stopped
SNPs and haplotypes - how many BPs per SNP, where is most variation, what is a haplotype, how does GWAS work to associate SNPs with phenotypes; difference between SNP and somatic mutation x2
4% difference between us and chimps, 0.1-0.5% difference between individuals; so one single nt polymorphism every 500-1000bp but only 1.5-2% of genome protein coding, most variation outside genes; variants helpful in DNA sequencing when you look at locus where multiple alleles known to occur, these single nucleotide polymorphisms inherited in blocks called haplotypes; genome wide association studies use micro-arrays of SNP variants to case and controls to identify SNPs with high degree of association with a certain phenotype
For example, at a specific base position in the human genome, the G nucleotide may appear in most individuals, but in a minority of individuals, the position is occupied by an A. This means that there is a SNP at this specific position, and the two possible nucleotide variations – G or A – are said to be the alleles for this specific position; SNPs are in the germline and some ppl think they must be present in >1% of population to count, so this is different from a point mutation acquired during life which would be a somatic mutation
nondisjunction and link to maternal age - what non-disjunction is, what this results in; why is this more likely with increasing maternal age and link to ts21
homologous chromosomes fail to segregate in meiosis i, sister chromatids in meiosis 2 or mitosis; uniparental disomy with both copies of chromosome from one parent, trisomy and monosomy; mature oocytes believed to have limited capacity for reloading cohesin and cohesin may be lost over time leading to incorrect microtubule kinetochore attachment and chromosome segregation errors, hence increased risk of down syndrome with age
DNA replication - initiating move, what are replication forks, leading vs lagging strand, direction of movement in each; 4 main polymerases, role of each; exonuclease activity of first type; second in complex with what trimer which is loaded by what and displaces what in what process; 5 steps ( last just for lagging strand, also which polymerase more on which strand)
nucleophillic attack of 3’-OH on alpha phosphate moiety of incoming dNTP with subsequent PPi hydrolysis driving the reversible reaction; occurs at replication forks which procede bidirectionally; semidiscontinous as okazaki showed by pulse labelling with radioactive thymine, leading strand continuous 5’ to 3’ and lagging strand discontinous fragments, each individually 5’ to 3’ with overall 3’ to 5’ movement
polymerases: alpha, delta, gamma and epsilon, all members of B family based on sequence homology (gamma is family A); alpha extends primer by 20nts then delta takes over on leading and lagging strands with processivity dependent on the PCNA DNA clamp; pol E also does leading strand and isnt dependent on PCNA; gamma is a family which replicates mitochondrial genome
alpha has no exonuclease activity and involved in extending primer so if it makes mistakes bases may be removed with primer anyway; delta in complex with PCNA trimer (proliferating cell nuclear antigen) sliding clamp which is a ring and is loaded by replication factor C RFC (1 large subunit and 4 small) and displaces pol alpha to allow delta to bind in template switching
topoisomerase unwinds, helicase breaks h bonds, DNA primase adds rna primer, then polymerase on leading and lagging strands (more epsilon on former and delta on latter), with latter having okazaki fragments stitched together by ligase
physical organisation of the genome - euchromatin is what, 3 charcteristics of where it is, replicated when and how much recombination; heterochromatin is what, x2 where, replicated when and how much recombination; link to x cr
euchromatin is less condensed, in chromosome arms, unique sequences, gene-rich, replicated throughout S phase and undergoes recombination in mitosis; heterochromatin highly condensed, centromeres and telomeres mainly, repetitive sequences, gene poor, replicated late in S phase with less recombination; dosage compensation of x to heterochromatin in females
structure of the human genome - 7 regions, what percent codes for proteins and what percent is gene footprint (inc 3 things), what are short tandem repeats (+how much of DNA are these, how big can they get, how do they arise, used in what), segmental duplications are how much of genome; what percent derived from transposons (inc 4 types, how they move, what this facilitates), mini and microsatellites inc why non-trinucleotide repeat expansion matched and triplet in Huntingtons and fragile X
sequences include centromeres and telomeres (latter a form of minisatellite DNA), origins of replication, matrix attachment regions (where DNA attaches to nuclear matrix), protein coding genes (enhancers - oft thousands of base pairs upstream of transcription, promoters - usually <200 base pairs upstream and containing TATA boxes and initiator, exons (each consisting of coding region and 5’ and 3’ untranslated regions that serve roles like mRNA transport, translation initiation, and attachment of polyA tail), introns (never translated bits between exons, some of which serve as miRNA (post-transcriptional regulation of gene expression etc); rna coding regions (rRNA, tRNA, other miRNAs and misc others)
then there are the repeated sequences of which there are satellites and interspersed sequences; former unique sequences repeated in one area that are either minisats (30-35bps) or microsats (2-5bps); some microsats are in coding regions and expansion of these trinuc repeats can cause disease(polyQ diseases, fragile X etc), but most are not in coding regions; latter are sequences which are dispersed across genome rather than in one area and may be short (13% of genome) or long (21% of genome); LINEs and SINEs are both retrotransposons (derived from RNA); besides LINEs and SINEs retrotransposons also inc endogenous retroviruses and the 3 together are >45% of genome
big compared to prokaryotes and less gene dense, genes interrupted with introns and lots of repetitive DNA; 2% genome coding for proteins, 25% gene footprint (promoters, exons, introns); some is heterochromatin eg centromeres; 3% of DNA short tandem repeats STRs eg CACA, TATATA arising from template slippage during replication and up to ~100bp, vary between individuals and used in DNA fingerprinting; segmental duplication of 10-300kB ~5% genome, also non-coding RNAs such as miRNAs
contains transposons: 45% of euchromatic genome in 100 to several thousand bp are transposon derived repeats, remnants of retrotransposons and most lost ability to mobilise: long interspersed nuclear elements (most inactive due to random mutations accumulated through generations, though some inserted into gene cause disease) short interspersed nuclear elements (parasitic DNA), retrotransposons with large terminal repeats, inactive copies of partially retrotransposed genes; these mobile genetic elements mean genome undergoing constant change as though many inactive some can move around the genome: DNA transposons moved by DNA transposase and retrotransposons DNA to RNA to DNA and inserted elsewhere in genome, facilitate appearance of new genes/patterns of gene expression so evolution
and satellite DNA: minisatellites tracts of repetitive DNA in eg telomeres/centromeres, microsatellites smaller (2,3 or 4 nts) unstable microsatellites may undergo trinucleotide repeat expansion which shows genetic anticipation (severity increases with generation number eg Huntingtons due to addition of CAG repeats), non-trinucleotide repeat expansion masked as causes frameshift leading to developmental lethality; CGG expansion within gene on x chromosome gives fragile X syndrome with intellectual disability
methods of DNA repair - stingle strand breaks (3), double strand breaks (2)
single strand breaks: base excision, nucleotide excision, mismatch repair
double strand breaks: non-homologous end joining, homologous recombination
digeorge syndrome - aka, genetic cause leading to defect where and how does this lead to impact on immunity, mnemonic for remembering features
DiGeorge syndrome, also called 22q11.2 deletion syndrome, results from a microdeletion in a portion of chromosome 22 that leads to a
developmental defect in the third pharyngeal pouch and third branchial arch. consequences include incomplete development of parathyroid glands and
the thymus gland. An underdeveloped thymus gland results in an inability to create functional T cells.
Features of DiGeorge syndrome can be remembered with the CATCH-22 mnemonic:
C – Congenital heart disease (conotruncal eg VSD)
A – Abnormal faces (characteristic facial appearance inc hypertelorism, low set ears, cleft palate)
T – Thymus gland incompletely developed
C – Cleft palate
H – Hypoparathyroidism and resulting Hypocalcaemia
22nd chromosome affected
klinefelters - appear as normal which gender until when, then develop what 9 features (which aspects of learning x2 esp affected), what improves many sx, what can potentially allow fertility, 2 more mx
Usually patients with Kleinfelter syndrome appear as normal males until puberty. At puberty can develop features suggestive of the condition:
Taller height
Wider hips
Gynaecomastia
Weaker muscles
Small testicles
Reduced libido
Shyness
Infertility
Subtle learning difficulties (particularly affecting speech and language)
finding of hypergonadotropic hypogonadism indicates primary gonadal failure: FSH elevation typically predominates over LH, though both are elevated above normal. Testosterone concentrations are usually low or low-normal in both adolescents and adults. Sex hormone-binding globulin (SHBG) tends to be elevated, which causes the free testosterone in the serum to be disproportionately low compared to the total testosterone. The majority of adults with KS will have hypogonadism, but not all. Serum estradiol is high-normal or elevated, but the estradiol/testosterone ratio is consistently elevated, which may explain the gynecomastia
Testosterone injections improve many of the symptoms
Advanced IVF techniques have the potential to allow fertility
Breast reduction surgery for cosmetic purposes
MDT input
klinefelter syndrome - genetic problem, frequency, apperance (5), genitals (4), intelligence (2)
47 XXY
1:1000 males
signs minimal before puberty; tall w long limbs, thin and feminine body shape, gynaecomastia in 40%, small/firm testes, small penis, maybe cryptorchidism, infertile, normal intelligence usually, may have problems in using/perceiving spolen language,
noonans - 9 appearance, 6 associated conditions (inc 3 eg for first condition)
Short stature
Broad forehead
Downward sloping eyes with ptosis
Hypertelorism (wide space between the eyes)
Prominent nasolabial folds/upturned nose
Low set ears
Webbed neck
Widely spaced nipples
Associated Conditions
Congenital heart disease, particularly pulmonary valve stenosis, hypertrophic cardiomyopathy and ASD
Cryptorchidism (undescended testes) can lead to infertility. Fertility is normal in women.
Learning disability
Bleeding disorders
Lymphoedema
Increased risk of leukaemia and neuroblastoma
noonan syndrome - inheritance, which gene/cr, karyotype, gender ratio, looks like what other condition and implication; stature, 4 facial features, common valve disease
AD, missense mutations in the PTPN11 gene on chromosome 12, normal karyotype, 1:1 M:F
phenotypically like turner syndrome, so if male and looks like turner think noonan
short stature, traingular facies, hypertelorism, epicanthic folds, thin upper lip, pulm stenosis
prader-willi (caused by loss of what/where, main rx strat), angelmans (4 features + 4 appearance)
Prader-Willi Syndrome is a genetic condition caused by the loss of functional genes on the proximal arm
of the chromosome 15 inherited from the father.
Growth hormone is indicated by NICE as a treatment for Prader-Willi Syndrome, aimed at improving muscle development and body composition
Angelmans: Delayed development and learning disability
Severe delay or absence of speech development
Coordination and balance problems (ataxia)
Fascination with water
Happy demeanour
fair skin/light hair/blue eyes/widely spaced teeth
genetics of angelman and prader-willi syndrome - what class of disorder, where is the problem, 2 ways to get for each
imprinting disorders due to del 15q11-13 - angelman syndrome if maternally derived deletion and prader-willi if paternally derived deletion; also if uniparental disomy with both cr15 from mum then prader willi and from dad then angelman, thus seems it is lack of normal mums resulting in angelmans and normal dads resulting in prader willi; this is half of cases, remainder due to other genetic abnormalities
angelmans - 6 appearance, 2 behaviour, 4 neurologic; prader willi - fetal growth, 4 appearance, 4 other features, problem later in life, 2mx
angelmans - microceph w brachyceph, fair hair/blue eyes, large tongue, prominent jaw, mental retardation, easily provoked paroxysms of laughter, seizures esp salaam attacks, slow wave cycles of 4-6s on eeg, hypotonic, stiff-legged broad based ataxic gait
pw - IUGR, short stature, almond eyes, long silky hair, small mouth w downturned corners, hypotonia, mental retardation, hypogonad, feeding problems from birth so initially small then pathological appetite at 2-3yo leading to obesity, later in life DM and cardiac disease - need strict dieting and lifestyle changes, GH can help with short stature; prone to temper tantrums
essential genetic pedigree knowledge (M vs F, affected vs carrier, arrow points to who, how to indicate deceased, twins (mono vs dizygotic); 2 carrier parents chance of affected, carrier, normal; consanguinous families and AR incidence, 5 egs, sex ratio for AR; AD parent % kids affected, mutation rate compared to AR, sex ratio, 6 egs; XLR sex ratio, offspring affect or carrir M vs F; XLD offspring pattern for affected M vs F, 2 egs; how to interpret likely pattern based on sex ratio (3), likely pattern if affected male beget affected male
male square, female circle; coloured in if affected, half coloured if recessive carrier
arrow points to the proband
diagonal line for deceased
diagonal line to two shapes means twins, if the shapes joined by a single line then monozygotic and if not dizygotic
AR has carrier parents, this couple would have 50% carrier, 25% affected, 25% normal
consanguinous families increase chances of AR conditions; M:F ratio 1:1; egs ae CF, sickle cell, beta thalasaemia, SMA, inborn errors of metabolism
AD: inherited from affected parent, half kids affacted and half normal, high spontaneous mutation rate compared to AR conditions, M:F ratio 1:1, greater variation in expression, eg hereditary spherocytosis, myotonic dystrophy, retinoblastoma, tub scler, friedreich ataxia, polycystic kidneys
x-linked recessive: males affected, but females may show features (eg prolonged clotting time in haemophilia or raised CPK in duchenne) due to x-inactivation; female carrier has half males affected and half females carriers, affected male has all male normal and half females carriers
x-linked dominant: affected fathers have normal sons and affected daughters, affected females pass to half their offsrping; often lethal to males so only females born; eg x-linked hypophosphataemic rickets, incontinentia pigmenti
if M:F ratio 1:1 likely AR/AD; if females more think x linked dom, if no females affected think x linked recessive; affected male beget affected male means AD likely - large pedigree may be needed to prove this vs x linked dom
A couple come for genetic counselling about the risk that their child will have cystic fibrosis. The husband’s sister has it, but the husband is not affected and there is no history in the wife’s family of the disease. Give answer as fraction
population rate 1 in 25 so assume wife has 1 in 25 chance of carrying
husbands parents must both be carriers, as he doesn’t have it then he must either be AA, Aa, or aA therefore 2/3 chance he is carrier
if both parents carries then chance of child being affected is 1/4
so answer is 1/25 * 2/3 * 1/4 = 2/300
chromosome analysis (number of pairs, how sorted in karyotype x3 factors with two things changing as move left to right, genetic test procedure (usually use what cell, what phase is cr arrested in for staining), general approach to analysing a karyotype (look for 3 things first), how to describe a chromosome pattern formally (3 things and eg for normal turner, klinefelter, cri du chat, how translocations are described)
23 pairs - 22 autosomes and one sex
sorted by size, positionof centromere, and banding pattern with top left side being large chromosomes with median placed centromeres - then left to right become smaller and centromere more distal to form acrocentric chromosomes
genetic testing most convenient with peripheral blood lymphocytes but almost any tissue can be used; arrest chromosomes in metaphase and stain them
look to see if missing a sex chromosome, has extra sex chromosomes, or has an extra autosome
to describe a chromosome pattern say total number, sex chromosome composition, then genetic abnorm eg normal is 46 XX, turner is 45 XO, klinefelter 47 XXY, cri du chat 46 XY, del (p5)
translocations are expressed as t(a;b)(p00;q00) where a and b are the numbers of the chromosomes involved and 00 are the break points
inheritance of down syndrome (risk at diff ages, most common cause, second-most common including what a parent may have (what their cr makeup is) and how that impacts risk in M vs F, third cause, AFP (checked when, 4 reasons high, 1 low; triple test uses what 2 other things and are they high or low; detection and false positive rate
risk is 1:2000 if mum 20yo, 1:700 if 30yo, 1:100 at 40 and 1:50 at 45yo
cause almost always (95%) non-disjunction during first meiotic division resulting in extra cr21, with 88% due to non-disjunction of maternal gamete and 8% non-disjunction of paternal gamete; in 2-3% of cases is instead a translocation
a robertsonian translocation is where long arms of two acrocentric cr fuse at the centromere, giving 45 chromosomes but unaltered (‘balanced’) genetic makeup so normal phenotype; however may have cr unbalanced offspring due to inheriting the extra long arm - it may either be attached to another cr, commonly cr 14, or to another version of itself (XXt21;21) giving an isochromosome
isochromosome - unbalanced structural abnormality in which the arms of the chromosome are mirror images of each other, so eg consists of f two copies of either the long (q) arm or the short (p) arm giving partial trisomy of the duplicated genes and partial monosomy of the deleted ones
in a child with unbalanced translocation causing down syndrome there is a 25% risk parent has balanced robertsonian translocation (commonly 45 XXt(21;14), with remaining 75% of the time it being de novo; hence if baby born with down syndrome due to translocation need to karyotype both parents
if the parent is carrying a balanced robertsonian translocation they have 1:4 chance of forming a down syndrome zygote, but also 1:4 chance of forming monosomic 21 zygote (as gets nothing from affected parent) which aborts, so risk of fetus carrying falls to 1:3 and many of these babies abort naturally meaning risk in carrier mother is actually 1:10, 2% risk if father (as sperm immotility results)
in 1% of cases down syndrome due to mosaicism, these children have milder phenotype; this is either due to a nondisjunction event during an early cell division leads to a fraction of the cells with trisomy 21 or when an anaphase lag of a chromosome 21 in a Down syndrome embryo leads to a fraction of euploid cells
maternal serum AFP taken at 16-18 weeks - high if NTDs, abdo wall defects, multiple pregnancies, intrauterine death; low in down syndrome; triple test also uses hCG (high) and unconjugated oestriol (low); 60% detection rate with 5% false positives
down syndrome antenatal diagnosis
All pregnant women to be offered screening for Down, Edwards and Patau
syndromes.
combined test can be performed when the baby’s crown rump length
(CRL) is between 45.0mm and 84.0mm. This is between 11+2 and 14+1
weeks. The nuchal translucency (NT) measurement is needed to calculate the
chance result. The blood sample can be taken from 10 weeks, but normally at the time of the 12 week scan
If the NT cannot be measured, or the CRL measurement is greater than 84.0mm, the woman is offered the quadruple test. If accepted, this test can be performed when the baby’s head circumference (HC) is between 101.0mm and 172.0mm. This is between 14+2 and 20+0 weeks. The blood sample can
be taken from 14+2 weeks but quadruple test is not as accurate as combined test
Women found to be higher chance for any of the syndromes to be offered the options of non-invasive prenatal testing (NIPT) and prenatal diagnosis (aka amniocentesis or CVS)
combined test uses maternal age, beta HCG (An increased level of bhCG in maternal blood in the first trimester is associated with Down’s syndrome. Conversely, a decreased level is associated with Edwards’ and Patau’s syndrome), PAPP-A (decreased level of PAPP-A in maternal blood in the first trimester is associated with Down’s syndrome (trisomy 21), Edwards’ syndrome (trisomy 18) and Patau’s syndrome (trisomy 13)), nuchal thickness and crown rump length
quadruple test only looks for down syndrome and looks at maternal age as well as for low AFP and unconjugated oestriol and high bHCG and inhibin A
chance cut off of 1 in 150 then applied, lower risk if < 1 in 150 and higher risk if > 1 in 150
NIPT assesses placental cell-free fetal DNA found in maternal blood and combines this with the mother’s background probability of a trisomy (mother’s age or the combined test results offered within the NHS) to obtain a likelihood ratio to predict whether or not the baby is more likely to have a chromosomal condition, to inform whether to proceed to diagnostic testing
CVS takes sample from placenta and is indicated at 11-14 weeks gestation and amniocentesis taking amniotic fluid >15 weeks; uncomfortable, 1 in 200 risk of miscarriage and 1 in 1000 risk of serious infection; normally obtained DNA sent for full karyotype and takes 2 weeks for these results to come back, fast-FISH can be done and get result in matter of days but only available privately
note can apply combined test separately to each baby in a pregnancy if dichorionic or provide one overall probability if monochorionic
down syndrome - number of births, height, IQ, 3 skull features, 3 eye features, 5 face features, 7 associated congenital conditions (inc ix needed before contact sports and 3 sx to beware), 2 neurological features, 5 features of hands/feet, increased risk of 3 conditions, how many die in first 5 years and main cause
1:800 live births
short, IQ oft <50, dev delat
brachycephaly, third fontanelle, delayed font closure
upward slanting palpebral fisures, epicanthic folds, cataracts
upturned nose, small ears, inc’d middle ear infections, downturned mouth, protruding tongue
inc’d risk of congen or autoimmune hypothyroid; atlanto-axial intability (beware neck pain, limb weakness, or paraesthesiae and screening x-ray before contact sports)
congen heart disease, esp AVSD; tracheo-oesopg atresia, duodenal atresia (double bubble), annular pancreas, hirchsprungs
hypotonia, 10% get epilepsy -10x prev of normal pop
short/broad hands, single palmar crease, clinodactyly; short broad feet w inc’d space between hallux and 2nd toe
increased risk of ALL, AD, rec resp infections from poor white cell function
15-20% die in first 5 years mainly due to CHD, many live into 60s or later
postnatal management of down syndrome
review: are they clinicall well?
if yes: karyotype and full cr analysis, FBC and film, Pre & Post Ductal saturations,
ECG & CXR. Echocardiogram within 6 weeks; chase newborn screen for congen hypothyroidism; Routine newborn hearing screen.Audiology F/U: 8mo.
- Routine ophthalmologic examination (during NIPE) and
ophthalmology referral on discharge for routine F/U
- Ensure Baby has opened bowels/passed urine
- Plot growth on the DS growth chart
-assess feeding, if poor then admit to neonatal unit, if satisfactory then discharge planning with neonatology clinic follow up and referral to community paediatric team
if clinically unwell are you worried about congen heart disease, duodenal atresia/bilious vomiting, poor feeding, resp distress, or re/post-ductal sat difference >3%
CV
Between 40 and 60% of babies with Down syndrome have congenital heart defects. Of
these 30 - 40% are complete atrioventricular septal defects (AVSD). Most AVSD can be
successfully treated if the diagnosis is made early and the baby referred for full corrective
surgery before irreversible pulmonary vascular disease (PVD) is established.
Haem
DCC performed but limited to 1 minute; All babies with suspected or confirmed Down syndrome should have a FBC and a Blood film
taken in the first 2-3 days of life, ideally at the same time as their genetic tests as Transient Abnormal Myelopoiesis (TAM) is a congenital leukaemia unique to neonates with
Down syndrome or mosaic trisomy 21 - Any neonate with a blast percentage of >10% and/or clinical features suggestive of TAM (bruises, bleeding easily, liver & Renal
impairment, infection) should be discussed urgently with the regional paediatric haematology centre and blood sent for GATA1 genetic testing
Sensation
OME present at birth in 35% of babies with TS21 and tenfold higher incidence of congenital cataract and infantile glaucoma
health assessment for child with down syndrome
Babies with DS should have neonatal screening undertaken prior to discharge as in other flashcard
they will then be followed up regularly in the community including full history of any respiratory, cardiac, or bowel symptoms and any concerns about vision and hearing, plus checking if any issues with sleep, plotting growth, and performing developmental assessment, plus from age 1 looking for evidence of cervical spine instability, middle ear disease, squint, cataract, nystagmus, nasolacrimal duct obstruction, blepharitis, and as child becomes older considering need for contraception (adolescent); careful auscultation of heart also indicated
complications to be aware of:
40% have CHD, AVSD commonest; duodenal atresia, hirschprungs disease, short stature, AML (normally between 1 and 5 yo, most commonly 2 yo) and ALL (more likely than AML after 3 and most cases by 6yo), 10% of DS kids will have some form of myeloproliferative disorder like temporary leukaemia that resolve within 3 mo
8% will have epilepsy with common patterns inc focal, infantile spasms, and GTCS
global dev delay with challenges in the expressive language domain compared with receptive language. IQ can range from mild to moderate intellectual disability, between 40 and 72
30-60% get OSA (recommended all children get sleep study between 3 and 4yo)
hearing loss, increased susceptibility to URTIs - if hospital admission, recurrent other infections, or infections severe may need immunodef screening and some areas will do basic immunodef screening for all DS patients
hypothyroidism in up to 20%, nasolacrimal duct obstruction due to midface hypoplasia, congenital cataracts, strabismus, delayed primary and secondary dentition and small mouth leading to crowding; coeliac disease in 7-16%, high incidence of seb derm and up to 9% have alopecia areata
ligamentous laxity and low muscle
tone may contribute to knee and hip problems, and increase susceptibility to subluxation and dislocations
ASD and ADHD may be seen; depression and dementia (in 50s) both as adults
About 15% of patients have lax atlanto-axial joint. This may result in spinal cord compression in 1% to 2% of cases.In terms of atlanto-axial subluxation, symptoms of myelopathy should be sought, including neck pain, changes in head positioning or torticollis, spasticity or change in tone, radiculopathy, incontinence, changes to gait (inc worsening mobility or frequent falls), or hyper-reflexia
